Re-write the tool

[bebatut]

I rewrote the tool:

• Add a CDS class to manage the CDS and their related variables
• Make smaller functions
• Cover the functions with unit tests
• Simplify launch of the tool with a shell script
• Add Makefile to help installation and test
• Add CircleCI for the tests

@keuv-grvl Can you have a look if you have some time? I will also ask Will

I need to test it on few real cases to be sure the results are the same (but should be given the unit tests). But I need a more stable internet connection (specially to download the reference db)

[codecov[bot]]

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@b771e10). Click here to learn what that means. The diff coverage is 99.75%.

@@            Coverage Diff            @@
##             master      #12   +/-   ##
=========================================
  Coverage          ?   99.75%           
=========================================
  Files             ?        5           
  Lines             ?      414           
  Branches          ?        0           
=========================================
  Hits              ?      413           
  Misses            ?        1           
  Partials          ?        0

Impacted Files	Coverage Δ
pylprotpredictor/check.py	100% <100%> (ø)
pylprotpredictor/write_report.py	100% <100%> (ø)
pylprotpredictor/predict.py	100% <100%> (ø)
pylprotpredictor/export.py	100% <100%> (ø)
pylprotpredictor/cds.py	99.64% <99.64%> (ø)

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update b771e10...420331b. Read the comment docs.

[keuv-grvl]

Your work with the tests is amazing @bebatut!

I made some suggestions about the sequence translation, I do not know if it is really relevant. I still have some doubts about the main executable (bin/PrylProtPredictor). I think we can make it more robust.

I will try to run your tests locally soon.

[bebatut]

I fixed more of your comments! I opened issues to fix other comments once the PR will be merged! I also added some docs!